Posted
by
samzenpus
on Thursday December 10, 2009 @05:40AM
from the kamikaze-gas dept.

MikeChino writes "Researchers at Arizona State University have genetically engineered cyanobacteria to dissolve from the inside out, making it easy to access the high-energy fats and biofuel byproducts located within. To do this they combined the bacteria's genes with genes from the bacteriaphage — a so-called 'mortal enemy' of bacteria that cause it to explode. Cyanobacteria have a higher yield potential than most biofuels currently being used, and this new strain eliminates the need for costly and energy intensive processing steps."

Plants are the most efficient at collecting solar energy. Plants are the most efficient at storing energy as some form of hydrocarbon. We already have a huge infrastructure to distribute hydrocarbons. It's such a perfect fit. This hydrogen nonsense was a huge waste of money, and should have been invested in biofuels.

*Ahem* the basic premise is wrong. Plants are NOT the most efficient at photosynthesis. In fact, plants, in the most narrow definition of the word, are incapable of photosynthesis.

Plant cells do, however, contain a degenerate cyanobacter, there are a few different species but we call all of them "chloroplasts". Strictly speaking this part of plant cells is not actually plant in origin.

Just like animal cells are not actually capable of digesting food, and using it to convert ADP into ATP. We do however conta

What are you smoking? *Ahem* the basic premise is wrong. In fact, plants, in the most narrow definition of the word, are totally fucking capable of photosynthesis. Unless you just made up a definition of a plant. You see, its because plant cells do contain a degenerate cyanobacter that we call a "chloroplast." Strictly speaking, this part of plant cells is not actually plant in origin, but then if we're speaking strictly, neither is the DNA in the plant cells or the cell membrane or the cell wall because, you see, all of these come from these really old bacteria and the plant just STOLE them! And called themselves living things! Ugh, it makes me sick. "Actually," it doesn't matter that chloroplasts, a long time ago, were fully alive. It's kind of like how it doesn't matter that you, a long time ago, were a small child with the promise of being a productive human being. Now, chloroplasts are part of plants and you are a piddling excuse of a man.

If you still don't believe me, consider: while chloroplasts were free-living cyanobacteria millions of years ago, they are now incapable of survival outside of the host cell; additionally, they cannot replicate without the host cell so they are "not actually 'fully' alive" either. Considering that a substantial portion of their DNA is also stored in the nucleus of the plant cell, one must really consider the chloroplast part of the host cell; that is why any biologist will say that chloroplasts are an organelle inside (some) plant cells. The same argument is applied to mitochondria: they are part of animal cells and thus, animal cells are alive. Trying to split the eukaryotic cells from mitochondria (or plant cells from chloroplasts) is like taking the creme filling out of a Twinkie; you can't because both parts are integral to the whole. Neither you nor your liver would survive very long without each other, and the same can be said for eukaryotic cells and mitochondria. (Obviously, this doesn't generalize to other organs as you are living proof that life can be sustained sans brain).

Needless to say, the cyanobacterium itself is not necessarily more efficient at photosynthesis than entire plant cells. For starters, all plant cell structures except for the chloroplasts are basically transparent so all the sunlight absorbed by plant leaves is absorbed in the chlorophyll that is only present in the cytochrome complexes in the chloroplasts. Additionally, plant leaves have other structures that control the environment inside the leaf and let the "cyanobacteria" work better; think of it as how "humans" work play WoW much better in air conditioning than hot sunlight. Normally, the plant-chloroplast relationship would be called symbiotic since the plant provides the chloroplast with otherwise unavailable access to sunlight. However, in this case it's direct human intervention that provides the access to sunlight. it obvious that the plant and chloroplast both benefit from their arrangement, but you are an idiot who styles himself a genius.

Also, can you please explain to me how it is "direct human intervention" that provides chloroplasts with sunlight? I didn't realize that we controlled the fucking sun...or is that because I one of the sheople manipulated by the secret cabal?

You basically beat me to what I was going to say, but I will also add that the OP neglected to mention that glycolysis, which certainly produces ATP, occurs in the cytoplasm of every animal and plant cell...how that would make them "not alive" I haven't the faintest idea.

Dang it! I wanted to mod parent up for such a well articulated explanation of cellular composition and some of the evolution behind it. But parent commented as AC.

Although I am not a biologist, I do remember reading some relatively new science that describes how the evolutionary trees of prokaryotes and eukaryotes first diverged, but then recombined. Thus, we have living cells that contain the elements of both.

But, I tagged this article with a 'whatcouldpossiblygowrong' tag because of the inevitable u

Needless to say, the cyanobacterium itself is not necessarily more efficient at photosynthesis than entire plant cells. For starters, all plant cell structures except for the chloroplasts are basically transparent so all the sunlight absorbed by plant leaves is absorbed in the chlorophyll that is only present in the cytochrome complexes in the chloroplasts.

I suspect the issue here is that it can be easier to get at something from inside a cyanobacterium than it is to get something from inside a plant cell

Additionally, producing plants is the only way we have of creating a net decrease in carbon while producing energy. Of course, this excludes damages done by irrigation, fertilizer runoff pollution, or whatever other bad things happen when we try to grow large quantities of plants where they wouldn't normally grow

Photosynthesis extracts a whole lot more of the sun's energy per square meter than our best solar panels..

No it doesn't. Most plants only operate at 1-2% photosynthetic efficiency, the most efficient crops maybe at 7%, and the theoretical maximum is 11% [wikipedia.org].

Compare that to solar cells which have 15-20%, in the laboratory even 40% efficiency. The advantage of photosynthesis is not efficiency, but price and resiliency, with the "cells" manufacturing themselves.

You are comparing turning the suns energy into electricity to turning the suns energy into hydrocarbons and then turning that into electricity, and you are discounting the other uses for the hydrocarbons.

Taking carbon out of the air and cracking water into hydrogen and oxygen takes a whole lot of energy and the plants do it better than they can in the lab, when the only energy input is the sun.

Taking carbon out of the air and cracking water into hydrogen and oxygen takes a whole lot of energy and the plants do it better than they can in the lab, when the only energy input is the sun.

Okay, that may be true, given your constraints. I think it also probably holds for carbon fixation from the atmosphere, by itself. But surely you're not claiming that a plant is more efficient at hydrogen production than a 25% efficient solar cell paired with a 50% efficient electrolysis process. So obviously we know how to do some parts of the process more efficiently already.

And atmospheric carbon fixation is something of a moot point when we have hundreds of years of reserves of carbon that we are alr

And atmospheric carbon fixation is something of a moot point when we have hundreds of years of reserves of carbon that we are already digging up out of the ground and expelling into the atmosphere as highly concentrated CO2. They will even pay you to take it.

Parent gets to the point. The advantages of plants are:
plants provide a service that "They will even pay you" for: pulling waste CO2 out of the atmosphere;
plants store solar energy;
plants manufacture themselves*;
waste oxygen from plants is an essential ingredient to animal life.

Disadvantages: plants are flammable when dry, some have potential to maim when knocked over, some taste icky, the larger ones can be navigation hazards, and many harbor undesirable organisms*.

No, the 11% max. figure is for just turning sun's energy into hydrocarbons. If you want to generate electricity out of it, like in a bio-mass power plant, the thermodynamic losses would be on top of that so the efficiency would be considerably lower.

It's all in how you look at it. If we deduct the energy needed to make more solar cells from the figure for PV, (since plants and bacteria use some of their energy for replication), photosynthesis looks pretty good.

That depends on what kind of PV cells you're using, since they vary greatly in both efficiency and cost. It's true that the up-front cost (both in terms of energy and materials) of PV cells is rather high, however, their 20+ year lifespan tends to amortize the initial investment nicely over time. Whereas if you're producing energy from plants, you have ongoing harvesting, processing, and distribution costs which may be comparable or greater than your initial investment in PV would have been.

I'm not saying PV is bad, or even that plants are better, just that the comparison is more complex than the raw conversion efficiency. Photosynthesis may make a lot of sense in large scale use, but probably isn't even practical for a residential application.

No it doesn't. Most plants only operate at 1-2% photosynthetic efficiency, the most efficient crops maybe at 7%, and the theoretical maximum is 11% [wikipedia.org].

Compare that to solar cells which have 15-20%, in the laboratory even 40% efficiency. The advantage of photosynthesis is not efficiency, but price and resiliency, with the "cells" manufacturing themselves.

We should also look at the overall efficiency including the end use. Combustion to produce mechanical energy is going to be less efficient tha

Yeah, but plants have the storage problem well handled. The electricity from your vaunted sand-panels must be used immediately or it is lost. Making hydrocarbons from electricity is far more expensive than making hydrocarbons from hydrocarbons, and the transportation sector will require hydrocarbons as a storage mechanism until electrical batteries can contain the same concentration of stored energy in both weight and volume and charging speed.

and the transportation sector will require hydrocarbons as a storage mechanism until electrical batteries can contain the same concentration of stored energy in both weight and volume and charging speed.

You might also want a battery which dosn't create more pollution to manufacture and dispose of than a fuel tank.

Plants are cheap. Land is not, processing plant material is not, dealing with plant waste and contaminants (some harmful) that can't be part of the fuel is a problem, fertilizer has it;s own environmental issues, water cost more than gas, and would you really truse a fuel shortage due to a bad frost???

Also, this is the exact reason ethanol is bad, gallons per acre per year is about 1% of the total earth's needs if we choose to continue to eat.

This is REAL, not vaporware. It's accepted simple chemisty, proven over 50 years of use, finally attacked and refined with modern improvements in heat exchangers, electrolizers, and more, plus being combined with wind energy (actually solving one of Wind's biggest issues, off-peak overproduction), and the enture process is carbon nuetral...

If you believe that, I have a really neat water-powered car to sell you... gets 8,000 miles per gallon, and even comes with an ice-cube dispenser.

I would expect in the future some kind of battery cells which directly interface with a massive array of plant-emulating light absorbing complexes which produce a voltage from sunlight.

Though in the Wikipedia I see (see 'photosynthesis') that this process converts light into energy with an efficiency of 3-6%, while solar panels have 6-20%, I believe that it might reach a point where mass production of hybrid organo-metallic devices can be achieved

Your point, though I suspect facetious, is quite interesting. I also envision a future where we can harness biological resources to produce energy. The mammalian brain produces megawatts of power over its lifetime. Imagine if we could take advantage of that? In envision a future where hundreds, perhaps thousands, if not millions or biological entities are connected in vast grids to power the world of the future. We could feed these batteries just as we feed chickens and pigs today; namely, just recycle the

Plants are the most efficient at collecting solar energy. Plants are the most efficient at storing energy as some form of hydrocarbon

I agree with you in that, but I don't think cyanobacteria are the only solution for biofuels.

Pond scum needs ponds, and ponds are filled with water. Granted, waste water can be used, these ponds can be part of a sewage treatment system.

I think a future biofuel system will be a more diverse system. We will need bacteria in ponds, but also other plants, such as cactuses or other that grow in semi-desert areas, for instance. Or what about the oceans? Imagine biofuel made from kelp, three quarters of the surface area of Earth are available for that.

I work upstairs from the ASU cyanobacteria project, and it is meant to be scaleable for the type of semi arid regions that you describe for cactus. Since cyanobacteria have very little vitamin and mineral requirements, they can be grown in large transparent tubes in the Arizona desert, pumped only full of tapwater and air.

Non-extremophile prokaryotic organisms, when given optimal growth conditions, will typically grow faster than most large eukaryotic plants, and in that lies the advantage of cyano over cac

Actually, using cyanobacteria can get around the scarce resource problem, because cyanobacteria are among the most efficient micro-organisms at growing in hypersaline, warm ocean (and salt flat) environments. In freshwater pond environments, one sees a progression of algae from diatoms (early in the growing season when the water's cold) to green algae, to cyanobacteria. Many researchers attribute this progression to the microcrustaceans' eating preferences, literally spitting out the cyanobacteria until e

Forget plants. Even at 10 times the lab yields, running 365 days a year, there simply isn't enough land. (lat along what to do with the biological wastes).

http://www.dotyenergy./ [www.dotyenergy.] Read everything they have. This is REAL technology that has been in use making Diesel and jetfuels since WWII. Modern improvements (over 60 approved aptents recently), combined with wind poewr, and design improvements for mass scale fuel manufacture make this work at about $60-80 per barrel depending on local markets (roughly

FYI: I an not an accosiate of doty energy, it;s investors, nor do I have a stake in the company, and am compensated in NO WAY for my comments.

Given the care and attention that you give to spelling and grammar, I'm not surprised that you're not being paid. In fact, if you're trying to encourage people to read what you're proposing (which doesn't sound an utterly incredible system, though I suspect that it's no where near as good as your summary), then you might find it better to use some writing tools to che

Comparatively speaking, the hydrogen economy is the unproven tech. Sure, we know fuel cells work well in spacecraft when maintained by an army of techs who don't care about the cost compared to gasoline, but how about when deployed in passenger cars maintained by people who may or may not have a high school diploma?

Actual production of the hydrogen is a giant hand-wave. Currently we use fossil fuel to produce affordable hydrogen. We have no infrastructure whatsoever that can even be refit to deliver the mas

Comparatively speaking, the hydrogen economy is the unproven tech. Sure, we know fuel cells work well in spacecraft when maintained by an army of techs who don't care about the cost compared to gasoline,

With spacecraft reducing weight is of great importance, so much so that they stopped painting the shuttle external tank white after the first few flights. This makes it worthwhile dealing with a difficult to handle fuel.

We have no infrastructure whatsoever that can even be refit to deliver the massive am

Not according to this fellow, who won an Ig Nobel award for his work with bacteria from panda poop, who need to process quite a lot of cellulose in their diet. Hydrogen is the biofuel these bacteria produce.

Perfect fit eh? It may be easier to transition from oil based fuels to biofuels, but that doesn't necessarily mean it's better in the long run. There are two main reasons why oil based fuels are bad - poor sustainability and harmful emissions. While using biofuels solves the first problem it leaves the second. AFAIK biofuels (generally speaking) aren't as harmful as normal petrol (gasoline for the americans) but are about the same or maybe slightly better than diesel (with a slight efficiency hit).
Hydroge

Ah, the kicker...
Biodiesel is better for the environment than diesel or gasoline. For one, with petrodiesel and gasoline, there is always a certain amount of sulfur and other pollutants from the refinement process that gets into the atmosphere. With coal, it's not just sulfur, but you have other chemicals, such as uranium (more radioactivity is spread into the atmosphere by coal-burning plants than by all the nuclear power plants in the world).
While hydrogen may be seen as a panacea:
(1) our infrastuctu

Hadn't thought about the storage problem for hydrogen, but regardless, I stand by my points

It really is a big issue, especially when it comes to storing the fuel on the vehicle. You can't pour hydrogen into a gas or diesel tank nor will it go into the wing of a jet airliner. Even though you can probably get all three types of internal combustion engine to run on hydrogen you'd have to redesign the fuel system from scratch. Liquid fuels are just easier to handle.

Hydrogen on the other hand has one emission - water. The problems with it at the moment is that we don't have the infrastructure for it and it is expensive to impliment.BR>With existing fuels a fairly simple tank is needed to store liquid fuel at ambient pressure and temperature. Any kind of hydrogen fuel tank is considerably more complex.

Viscount Leverhulme famously said "Half my advertising money is wasted. The problem is that I don't know which half!" I believe that the same principle applies to funding scientific research.

You never know which approach is going to have the most commercial potential until you've gone and explored all the available approaches. Funding the ones that don't pan out is not a waste of money. It's part of the process that brings out the ones that do.

Plants also have a drawback: They need room. Incidentally the room where plants can grow. Plants we eat. There are already countries where people are suffering because areas that used to be used for crop planting are now used to create biofuel (mostly for export).

Hydrogen, being essentially created by electrolytic splitting of water, can be created anywhere where electricity can be produced in quantity and cheaply. Iceland comes to mind, with their geothermal energy they can (and do) create a surplus of ele

Not necessarily. You can take non-arable land, such as a desert, add sewage waste and bacteria, and VIOLA! biofuel. Or unused coastline, add fast-growing kelp and a lot of sunlight, regular harvests, and, again VOILA! biofuel. Both examples do not detract from current land use, and the coastline kelp forests may attract wildlife. That is not saying that arable land might be used for biofuel production...unless you tightly regulate the production, this will eventually happen if the profit from the sale of bi

Probably not. [wikipedia.org] I suppose you could say it is open to debate, but the consensus seems to be for positive energy output with current methods. Also perhaps worth noting is that the parent commented on biofuels in general, whereas you focused in on one particular biofuel from a source that happens to be a bad idea pretty much all the way around. I can see the rationale for using surplus corn for ethanol if you have to use it (the surplus corn).

As soon as even one or two bacteria manage to throw the phage-genes out again or, even simpler, acquire a loss-of-function mutation they'll have a huge advantage over the self-destructing ones and might eventually eliminate them. The result would be quite nasty for those who run the harvesting plant...

I'd at least suggest seperated smaller tanks of bacteria that are isolated from one another so that the damage of such an event is kept at a minimum.

As soon as even one or two bacteria manage to throw the phage-genes out again or, even simpler, acquire a loss-of-function mutation they'll have a huge advantage over the self-destructing ones and might eventually eliminate them. The result would be quite nasty for those who run the harvesting plant...

I'd at least suggest seperated smaller tanks of bacteria that are isolated from one another so that the damage of such an event is kept at a minimum.

It makes some sense. The idea is that whenever you have a lot of bacteria reproducing, mutation rates being what they are, benefitial mutations will eventually appear. Something like this has been used to. Chemostats [wikipedia.org], which are what these things will essentially be, have been used to test evolution experimentally in just this way.

Now, the flaw in Niedi's reasoning is that evolution is directed only be better differential reproduction. So, if bacteria reproduce before self-destruction, there will be no environmental pressure to select against this feature.

It makes some sense. The idea is that whenever you have a lot of bacteria reproducing, mutation rates being what they are, benefitial mutations will eventually appear. Chemostats [wikipedia.org], which are what these reactors will essentially be, have been used to test evolution experimentally in just this way.

Now, the flaw in Niedi's reasoning is that evolution is directed only to better differential reproduction. So, if bacteria reproduce before self-de

<quote>Now, the flaw in Niedi's reasoning is that evolution is directed only to better differential reproduction. So, if bacteria reproduce before self-destruction, there will be no environmental pressure to select against this feature.</quote>

bacteria usually keep on deviding (reproducing) themselves for an extremely long time, so I suppose the self-destructing genes will lead to premature death -> less reproduction in total compared to "normal" bacteria

Bacteria is not isolated organisms, most bacteria can not be breed as a singleton. That is because most species of bacteria is a colony living organism and they communicate with each other through the substances that they release in the environment which can signal among other things the concentration of nutrients.

At low levels of nutrients they will stop reproducing hence when the solution is saturated of bio-fuel bacteria the self-destruction gene can be triggered and the fuel harvested. This way there

So, if bacteria reproduce before self-destruction, there will be no environmental pressure to select against this feature.

Not so. Even if bacteria reproduce before self-destruction, if a bacteria that does not self destruct is more fit (even if the fact that it does not self destruct does not contribute to it's fitness) then the "don't self destruct" variant will become dominant.

As soon as even one or two bacteria manage to throw the phage-genes out again or, even simpler, acquire a loss-of-function mutation they'll have a huge advantage over the self-destructing ones and might eventually eliminate them. The result would be quite nasty for those who run the harvesting plant...

The selective pressure to maintain such a mutation would be in the processing stage where they add the nickel to make them self destruct. You can avoid that by not returning any waste from the processing stage back into the growth tank.

Of course, it's possible that the bacteria without the mutation may out-reproduce the ones with the mutation in the growth tank, but then you'd just start with a fresh batch of your preferred strain.

The Problem arises when you have a processing stage that runs continously and is not emptied, cleaned and refilled inbetween. You might get a culture in there that interfers with your fuel-harvesting.And let's just hope that they will not out-reproduce them in the growth-tank, cleaning everything and starting a fresh culture can be a royal pain. Plus it takes some time (thaw them, wait till they recover from the freezing and start reproducing again, wait till you have a sufficient density) which means lost

Based on the reporting of the article, I don't think that is the case. Mature the pool, divide it into a harvest and a non-harvest, nickle the harvest pool, drain the oil-y goodness + muck, clean, introduce non-harvest pool, wait for population to recover, repeat. Survivors of the nickle-apocalypse are not given a chance to return to the non-harvest population.

This is really cool because (if it can be scaled) neatly solves most of the issues with algal biodiesel. The only remaining problem is separating

A loss of function mutation in a yeast used for brewing or a yogurt culture would be a big problem, just not as sensational as a kill the consumer mutation. Yet maintenance and selective breeding of cultures has been manageable for centuries now.

By the time the survival aspect of the modification can come into play, the bacteria are already at a dead end. They are in the batch that is being processed to fuel. The survivors of the nickle treatment will be destroyed just as surely as those that didn't mutate. Yields will be monitored. A tank whose yield declines will be sterilized and re-seeded. Culture sources with poor yields will be destroyed and replaced by others that have bred true (or at least haven't mutated in a way we don't like), just like yeast cultures. Those that produce bad beer are destroyed.

Yes, they mutate a lot. Most of the mutations are a disadvantage. Of the remainder, most don't matter at all. Those that prove harmful to the purpose we culture them for are destroyed batch by batch. The very few that prove beneficial to our purposes are propagated.

In many ways, culturing for fuel production is easier. Unlike foods, we don't care if it has an "off" taste, just that it burns well after processing.

Consider, a brewing yeast that mutates so that it can oxidize alcohol for energy will find plentiful food as the others die out. By the end of the fermentation process they will easily dominate. However, they will produce nasty tasting beer. If the mutation happens in the culture rather than in the vat, the whole culture is discarded.

I'd wondered from the first article, how can a bacteria grow and reproduce
at the same time as dissolving. It doesn't of course, they need to
add a trace of nickel to start the cells dissolving and releasing there
fats. All very good. But 2 more years of research before it even gets
close to testing for commercial purposes. Shame we can't get this
sort of research done quicker, cheap energy is always something
we need, I wonder what the final price and conversion efficiency
will be?